Ahh.. substrate changes.
You could do a little bit at a time, swapping a few handfulls a day. You shouldn't upset the cycle any, but I would wait until the end of it anyway. Hands in the tank tend to be pretty stressful for fish, and so is the cycle, so if you can stand it a few more weeks I would wait.
When you do decide to start, there are two ways I can think of to do it: Both start with a little planning. If you want gravel, thats cool. If you want a sandy type substrate, thats cool too. (Sandy types are better for live plants, in my opinion. They require a little different kinda care, but not harder.) If you think you might like to have live plants, do a little research. (not hard at all, but saves you from doing this all again). Substrate additives, how much to put in, ect.
#1: (Bucket method) get a big huge bucket that will hold most or all of the water in the tank. K mart has a big tub that holds 20 gal for 5 or 6 bucks. (just make sure it's clean! nothing that looks like it was spilled in it, and wash it out with water and a little vinegar and rinse really well (no soap!). Siphon about half of the tank water out of the tank and into the tub/bucket, then start taking stuff out of the tank and putting it out of the bucket. Fish, fake plants, ect. Keep your filter media wet, but it doesn't have to be in the big bucket. When I changed my substrate, the filter media went into my water change bucket, fish went into the big one. (don't change the media for a few weeks prior to changing substrate.) That way, the good bacteria in it don't die. Take all the offending gravel out of the tank, but leave the gunk that gets trapped in it behind. (it's called "mulm", but I have no idea why it is called that) it is bacteria rich, and will help to avoid another mini-cycle later on. Rinse your new gravel well, put it into the tank, and then add the water from the big bucket to the tank. Add your fish, and test daily for ammonia, nitrites, ect. Sometimes a you might get a small spike in those. (cure with water changes)
The other alternative is simpler: just remove a bit of the old gravel at a time, then add the same amount of new gravel.. only bad part is you don't get a chance to totally re-arrange things, and you will never get that last bit of old gravel out. Simpler, but slower.